What is the resolution of your data? I have been able to get a solution for my protein with 30% identity but my resolution of data was 1.4 Angs. I believe to get a solution at 18% identity your search model has to be very close, like using Robetta to make the 3 mer and 9mer peptides and then work from a homology model. But your resolution should be around 1 angstrom.
On Fri, Dec 12, 2014 at 2:38 PM, Ursula Schulze-Gahmen < uschulze-gah...@lbl.gov> wrote: > > I am trying molecular replacement with a very poor model. The model > consists mainly of 1 long helix and two slightly bent antiparallel helices. > After dividing it into 2 fragments, I was able to find a solution for one > of the fragments ( at least I think so after looking at maps, packing, > refinement etc). But even if I place the first solution as fixed ensemble > in phaser, I cannot find a solution for the second fragment ( 18% sequence > identity). From the structure of the model and the packing it seems clear > where the fragment should go roughly. > > Are there any other programs other than phaser that might be able to solve > this problem? I tried already epmr and mr_rosetta without success. > I also tried to just superimpose the complete model onto the partial > solution. This results in quite nice packing, but doesn't refine. Is there > a rigid program refinement program with very large convergence? > > Ursula > > -- > Ursula Schulze-Gahmen, Ph.D. > Project Scientist > UC Berkeley, QB3 > 360 Stanley Hall #3220 > Berkeley, CA 94720-3220 > (510) 643 9491 >
